Gene Report

Basic information

Related studies

Functional annotation

Related other genetic factors

Overlap with SZ and MDD

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Basic Info

Approved Symbol	PER2
Symbol Alias	KIAA0347
Approved Name	period circadian clock 2
Previous Name	period (Drosophila) homolog 2, "period homolog 2 (Drosophila)"
Location	2q37.3
Position	chr2:238244038-238290102, -1
External Links	HGNC: 8846 Entrez Gene: 8864 Ensembl: ENSG00000132326 UCSC: uc002vyc.3
No. of Studies	7 (Positive: 1; Negative: 6; trend: 0)
Overlap with SZ?	YES
Overlap with MDD?	YES

Gene related studies (count: 7)

Reference	Tested Markers	Statistical Values/Author Comments	Result Category	Comment on Study
Kripke, D. F.,2009	SNP: rs2304669, rs2304672, rs4663868	Significant association was observed in the BP group.	Positive	Comment on Study
Byrne, E. M., 2014		P-value=0.45. Gene-based tests show no significant association between this gene and BD.	Negative	Comment on Study
Nievergelt, C. M., 2006		Single SNP TDT analyses showed no evidence for association to BPAD.	Negative	Comment on Study
Shiino, Y.,2003	Other variant: PER2_2087A/G, PER2_2114G/A, PER2_2117G/A	Polymorphism on the CKIepsilon binding region of hper2 gene which was previously reported, is unlikely to play an important role in the development of bipolar disorder.	Negative	Comment on Study
Mansour, H. A., 2006		No significant association was detected in any sample using any test.	Negative	Comment on Study
Mansour, H. A.,2009	SNP: rs2304672, rs2304674	Gene-based tests:X<sup>2</sup>=7.226, P-value = 0.062 in recessive model, X<sup>2</sup>=3.587, P-value = 0.336 in additive model, X<sup>2</sup>=1.828, P-value = 0.849 in dominant model in BPI. No significant association was observed using neither single SNP-based analyses nor gene-based tests in BPI.	Negative	Comment on Study
Soria, V.,2010	SNP: rs2304673	No significant associations of PER2 gene were found in BPD patients.	Negative	Comment on Study

Gene functional annotation

Gene related GO terms (count: 44)

GO terms by PBA (count: 2)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0004871	signal transducer activity	molecular function	IEA	32
GO:0005634	nucleus	cellular component	IDA[22274616]; ISS	283

GO terms by database search (count: 42)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0097167	circadian regulation of translation	biological process	ISS	2
GO:0005737	cytoplasm	cellular component	IDA	322
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	biological process	ISS	62
GO:0042826	histone deacetylase binding	molecular function	IEA	13
GO:0019229	regulation of vasoconstriction	biological process	ISS	10
GO:0002931	response to ischemia	biological process	ISS	4
GO:0001222	transcription corepressor binding	molecular function	IEA	3
GO:0006351	transcription, DNA-templated	biological process	IEA	103
GO:0070063	RNA polymerase binding	molecular function	IEA	1
GO:0006631	fatty acid metabolic process	biological process	ISS	6
GO:0005515	protein binding	molecular function	IPI[22274616]	563
GO:0050872	white fat cell differentiation	biological process	ISS	3
GO:0051946	regulation of glutamate uptake involved in transmission of nerve impulse	biological process	ISS	1
GO:0036002	pre-mRNA binding	molecular function	IEA	1
GO:0031397	negative regulation of protein ubiquitination	biological process	ISS	6
GO:2000678	negative regulation of transcription regulatory region DNA binding	biological process	ISS	1
GO:0043130	ubiquitin binding	molecular function	ISS	5
GO:0019249	lactate biosynthetic process	biological process	ISS	1
GO:0001047	core promoter binding	molecular function	IEA	8
GO:0042754	negative regulation of circadian rhythm	biological process	ISS	3
GO:0070932	histone H3 deacetylation	biological process	ISS	4
GO:0000976	transcription regulatory region sequence-specific DNA binding	molecular function	ISS	4
GO:0045892	negative regulation of transcription, DNA-templated	biological process	ISS	43
GO:0000989	transcription factor binding transcription factor activity	molecular function	ISS	4
GO:0050796	regulation of insulin secretion	biological process	ISS	24
GO:0042752	regulation of circadian rhythm	biological process	ISS	12
GO:0007165	signal transduction	biological process	IEA	136
GO:0035257	nuclear hormone receptor binding	molecular function	IEA	5
GO:0003713	transcription coactivator activity	molecular function	ISS	22
GO:0070345	negative regulation of fat cell proliferation	biological process	ISS	1
GO:0006094	gluconeogenesis	biological process	ISS	4
GO:0032922	circadian regulation of gene expression	biological process	ISS	22
GO:0048471	perinuclear region of cytoplasm	cellular component	IEA	50
GO:0050767	regulation of neurogenesis	biological process	ISS	3
GO:0007623	circadian rhythm	biological process	TAS	40
GO:0005730	nucleolus	cellular component	IEA	28
GO:0019900	kinase binding	molecular function	IEA	8
GO:0005654	nucleoplasm	cellular component	IDA	163
GO:0005978	glycogen biosynthetic process	biological process	ISS	4
GO:0051726	regulation of cell cycle	biological process	ISS	6
GO:1990226	histone methyltransferase binding	molecular function	IEA	1
GO:0060567	negative regulation of DNA-templated transcription, termination	biological process	IEA	1

Gene related KEGG pathways (count: 1)

KEGG pathways by PBA (count: 0)

KEGG pathways by database search (count: 1)

ID	Name	No. of Genes in BDgene	Brief Description
hsa04710	Circadian rhythm	11

Gene related BioCarta pathways (count: 0)

Gene related interactors from protein-protein interactions data in HPRD (count: 1)

Gene	Interactor	Interactor in BDgene?	Experiment Type	PMID
PER2	PER3	YES	in vivo	10837028

Related other genetic factors

Gene related SNPs (count: 21)

Literature-origin SNPs (count: 5)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs2304669	chr2:238257022 - 238257022(1)	downstream_gene_variant; synonymous_variant	1(1/0/0)
rs2304674	chr2:238273263 - 238273263(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant	1(0/1/0)
rs2304673	chr2:238277281 - 238277281(1)	intron_variant; non_coding_transcript_variant	1(0/1/0)
rs2304672	chr2:238277948 - 238277948(1)	5_prime_UTR_variant; upstream_gene_variant	2(1/1/0)
rs4663868	chr2:238252450 - 238252450(1)	intron_variant; non_coding_transcript_variant	1(1/0/0)

LD-proxies (count: 16)

rs_ID	Location	Functional Annotation
rs11892306	chr2:238279838 - 238279838(1)	intron_variant; upstream_gene_variant
rs11892309	chr2:238279852 - 238279852(1)	intron_variant; upstream_gene_variant
rs4617993	chr2:238294273 - 238294273(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs3739064	chr2:238267745 - 238267745(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs1972874	chr2:238269761 - 238269761(1)	intron_variant; non_coding_transcript_variant
rs6754875	chr2:238284578 - 238284578(1)	intron_variant; upstream_gene_variant
rs13002160	chr2:238293490 - 238293490(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs2304668	chr2:238259807 - 238259807(1)	downstream_gene_variant; intron_variant
rs4663866	chr2:238242174 - 238242174(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs13026475	chr2:238269814 - 238269814(1)	intron_variant; non_coding_transcript_variant
rs4663299	chr2:238266434 - 238266434(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs13033501	chr2:238273219 - 238273219(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant
rs6741269	chr2:238270777 - 238270777(1)	intron_variant; non_coding_transcript_variant
rs4663301	chr2:238294521 - 238294521(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs35390666	chr2:238284937 - 238284937(1)	intron_variant; upstream_gene_variant
rs2304670	chr2:238256995 - 238256995(1)	downstream_gene_variant; synonymous_variant

Gene related CNVs (count: 0)

Gene related other variants (count: 3)

Variant Name	Variant Type	No. of Studies (Positive/Negative/Trend)
PER2_2117G/A	point mutation	1 (0/1/0)
PER2_2087A/G	point mutation	1 (0/1/0)
PER2_2114G/A	point mutation	1 (0/1/0)

Gene related regions (count: 4)

Region Name	Position	No. of Studies (Positive/Negative/Trend)
2q37-2qter	chr2:230100000-242193529	1 (0/0/1)
2q37	chr2:230100000-242193529	1 (0/1/0)
2q37.3	chr2:236400000-242193529	1 (0/1/0)
Chr 2	chr2:0-242193529	3 (0/3/0)

Overlap with schizophrenia (SZ) and major depressive disorder (MDD)

Gene relationship with SZ

Overlap with SZ from cross-disorder studies (count: 2)

Reference	Description	Result Category
19839995	Gene-based tests:X<sup>2</sup>=6.944, P-value = 0.068 in recessive model in SZ/SZA, X<sup>2</sup>=4.563, P-value = 0.209 in additive model in SZ/SZA, X<sup>2</sup>=1.671, P-value = 0.769 in dominant model in SZ/SZA. Association was observed using single SNP-based analyses while no association was observed using gene-based tests in SZ/SZA.	Positive
24687905	P-value=0.52. Gene-based tests show no significant association between this gene and SZ.	Negative

Overlap with SZ from candidate gene intersection analysis (count: 2)

Reference	ID in SZGene	Result Category
19839995	283	Positive
16507006	283	Negative

Gene relationship with MDD

Overlap with MDD from cross-disorder studies (count: 2)

Reference	Description	Category in MDD
24687905	P-value=0.67. Gene-based tests show no significant association between this gene and MDD.	Negative
20072116	No significant associations of PER2 gene were found in MDD patients.	Positive

Overlap with MDD from candidate gene intersection analysis (count: 0)

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Region: chr2:238244038..238290102 View in gBrowse